Highly automated capillary electrophoresis system

ABSTRACT

The invention is an improved multiplex capillary electrophoresis instrument or module with at least four and preferably six user-accessible vertically stacked drawers. An x-z stage moves samples from the user accessible drawers to the capillary array for analysis. An additional mechanical stage moves the array from side-to-side. The x-z stage, coupled with the additional array stage allows the system to sample all wells of a 384 well plate with a 96-capillary array. A computer program allows users to add capillary electrophoresis jobs to a queue corresponding to the analysis of rows or plates of samples without stopping or interrupting runs in progress.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.14/983,985, filed Dec. 30, 2015, which is a continuation-in-part andclaims the benefit of the filing date of earlier filed, commonly owned,co-pending application U.S. Ser. No. 14/822,956, filed Aug. 11, 2015,which itself is a continuation of U.S. Ser. No. 13/470,870, filed May14, 2012, now U.S. Pat. No. 9,140,666, issued Sep. 22, 2015, whichclaims the benefit of provisional application Ser. No. 61/643,411, filedMay 7, 2012, and is a continuation-in-part of design application U.S.Ser. No. 29/421,549, filed Mar. 15, 2012, now Design Pat. No. D689,621,issued Sep. 10, 2013.

BACKGROUND OF THE INVENTION Field of the Invention

This invention relates to a system and software for multi-channelcapillary electrophoresis.

Description of Related Art

The current next-generation sequencing (NGS) platforms use a variety oftechnologies for sequencing, including pyrosequencing, ion-sequencing,sequencing by synthesis, or sequencing by ligation. Although thesetechnologies have some minor variations, they all have a generallycommon DNA library preparation procedure, which includes genomic DNAquality & quality assessment, DNA fragmentation and sizing (involvingmechanical shearing, sonication, nebulization, or enzyme digestion), DNArepair and end polishing, and a last step of platform-specific adaptorligation. With a rapidly growing demand for DNA sequence information,there is a critical need to reduce the time required for the preparationof DNA libraries.

A labor-intensive step in DNA library preparation is the qualification(size determination) and quantification of both un-sheared genomic DNAand downstream fragmented DNA. Existing methods for DNA fragmentanalysis include agarose gel electrophoresis, capillary electrophoresis,and chip-based electrophoresis. Agarose gel electrophoresis is laborintensive, requiring gel preparation, sample transfer via pipetting, andimage analysis. The images obtained by agarose electrophoresis are oftendistorted, resulting in questionable or unreliable data. It isimpossible to use agarose gel electrophoresis for accuratequantification of DNA, which means that a separate, second method (UV orfluorescence spectroscopy) is required for quantification. Finally,agarose gel electrophoresis is difficult to automate. Chip or micro-chipbased electrophoresis provides an improvement in data quality overagarose gel electrophoresis but is still labor intensive. For example,chip-based methods require manual steps to load gel, markers andsamples. Even though these microchip or chip based electrophoresis unitscan run a single sample in seconds or minutes, the sample and gelloading are barriers to ease-of-use, especially when running hundreds orthousands of samples. Also, existing chip-based systems are unable toquantify genomic DNA. Capillary electrophoresis (CE) offers advantagesover both agarose electrophoresis and microchip electrophoresis in thatgel-fill and sample loading is automated.

Multiplex capillary electrophoresis is known. For example Kennedy andKurt in U.S. Pat. No. 6,833,062 describe a multiplex absorbance basedcapillary electrophoresis system and method. Yeung et al. in U.S. Pat.No. 5,324,401 describe a multiplex fluorescent based capillaryelectrophoresis system. Although these systems offer the advantage ofanalyzing multiple samples simultaneously, and can run several platessequentially, they lack the ability to load or change multiple sampleplates while the system is running, and they also lack a simple workflowfor efficient sample analysis.

While existing commercial CE systems can be automated with a roboticsystem, stand-alone systems are not fully automated or lack thesensitivity and data quality required for adequate DNA library analysis.An example of a CE instrument with a robot-capable interface is given byKurt et al. in U.S. Pat. No. 7,118,659. For the construction of DNAlibraries, as well as other applications such as mutation detection, itis often necessary to run thousands of samples per day, but theimplementation of an external robotic system for sample handling isprohibitively expensive, and many labs lack the expertise necessary forthe maintenance and operation of sophisticated robotic systems.Automated forms of micro-slab-gel electrophoresis have been developed,such as those described in United States Patent Application number20100126857. These allow for automatic analysis of multiple samples, butthe techniques either still require significant human intervention, orthey do not have the throughput required for high-volume applications.Amirkhanian et al. in U.S. Pat. No. 6,828,567 describe a 12-channelmultiplex capillary electrophoresis system capable of measuring up 12samples at a time using multiplex capillary electrophoresis. However,this system is not capable of measuring multiple 96-well or 384well-plates, and does not have the workflow that allows the analysis ofthousands of samples per day.

As can be seen, there a need for an automated capillary electrophoresissystem that a) eliminates the complexity, cost, and required expertiseof an external robotic system b) enables users to run from one toseveral thousand samples per day and c) allows users to convenientlyload several plates or samples onto a capillary electrophoresis systemwhile the system is running other samples and d) has the small size andfootprint of a stand-alone capillary electrophoresis unit.

This invention has as a primary objective the fulfillment of the abovedescribed needs.

BRIEF SUMMARY OF THE INVENTION

The present invention is a multiplex capillary electrophoresis systemand console with an improved sample handling and control method for theanalysis of samples.

One embodiment of the invention is a console with a series of at leastfour and preferably at least six vertically stacked user-accessibledrawers that can each hold a plate containing from 1 to 384 samplewells. Preferably, each user accessible drawer holds a sample platecontaining 96 sample wells. The system is configured so that sampleplates can be loaded onto the system at any time, including during theelectrophoresis or analysis of samples. User “A” can walk up to themachine, load a row of 12 samples, enter loading and analysisinstructions onto the computer and walk away. While user “A” samples arerunning, user “B” can walk up to the machine, load a tray of 96 samples,enter loading and analysis instructions and walk away. User “C” can walkup to the machine, load 12 samples, while either user “A” or user “B”samples are running, enter loading and analysis instructions, and walkaway. Two of the preferred six user-accessible drawers are used to holdan electrophoresis run buffer and a waste tray.

An alternate example system configuration allows user “A” to walk up tothe machine, load a 384 well tray, enter loading and analysisinstructions onto the computer and walk away. While user “A” samples arerunning, user “B” can walk up to the machine, load a tray of 384samples, enter loading and analysis instructions and walk away. User “C”can walk up to the machine, load 384 samples, while either user “A” oruser “B” samples are running, enter loading and analysis instructions,and walk away.

Another embodiment of the invention is a mechanical stage thattransports sample trays and/or buffer or waste trays from any one of thevertically stacked user-accessible drawers to the injection electrodesand capillary tips of the multiplex capillary array of the capillaryelectrophoresis subsystem.

Another embodiment of the invention is the placement of the capillaryarray on a mechanical stage that can shift the array left or right by afew millimeters each way, which, when coupled with the sample tray x-zstage of the present invention allows the system to access all wells ofa 384 well plate with a 96-capillary array. Access to all wells of the384 well plate is accomplished via movement of both the plate and thecapillary array. Another embodiment of the invention is a binding of thecapillaries and electrodes of each element on the sample plate side of amultiplex capillary array, so that the electrode/capillary combinationcan access the relatively small hole diameter of each well of a 384-wellplate without collision of the capillaries or electrodes with the sidesof the wells.

Another embodiment of the invention is a configuration and geometry ofthe electrophoresis console that allows for easy integration with anexternal robotic system. Existing electrophoresis systems based onmicrochips are not ideally suited for robotic arm integration, becausethey require significant manual intervention, including the need tochange chips frequently and the requirement of a manual pipetting gels,ladders, and sample into several different locations on a microchip.Other systems, not based on microchips, do not have easily accessible,vertically stacked drawers for easy access by robotic arms.

Yet another embodiment of the invention is the use of an x-z internalmechanical stage that.

-   -   a) transports sample trays and/or buffer or waste trays from any        one of the vertically stacked user-accessible drawers to the        injection electrodes and capillary tips of the multiplex        capillary array of the capillary electrophoresis subsystem    -   b) pushes any drawer out of the electrophoresis console, so that        an external robotic arm may pick up or replace tray from an        occupied drawer, or place a tray onto an empty drawer.

Another embodiment of the invention uses a computer program that enablesa user to create a queue of jobs, with each job representing an analysisof a new set of samples. This computer system enables users to enter jobdata even when the system is running samples. For example, user “A”loads “sample plate 1” into the system into Drawer 3 and uses a computerprogram to add a job to a queue, the job representing the injection andcapillary electrophoresis of samples in “sample plate 1” in Drawer 3.While the system is running user A's samples, user B loads plate 2 intoDrawer 4 and uses the same computer program to add a job to a queue, thejob representing the injection and capillary electrophoresis of samplesin “sample plate 2” in Drawer 4. User C loads “sample plate 3” intoDrawer 5 and uses the same computer program to add a job to the queue,the job representing the injection and capillary electrophoresis ofsamples in “sample plate 3” in Drawer 5.

A preferred embodiment of this invention is a system capable of allowingthe user to enter 24 or more individual jobs to a queue, with each jobrepresenting an injection and analysis of a plurality of samples.

An even more preferred embodiment is a system capable of allowing theuser to enter 48 or more individual jobs to a queue, with each jobrepresenting an injection and analysis of a plurality of samples.

Another embodiment is a system capable of allowing the user to enter 100or more individual jobs to a queue, with each job representing aninjection and analysis of a plurality of samples.

BRIEF SUMMARY OF THE DRAWINGS

FIG. 1 shows a left-front-view of the instrument, with 6 drawers forholding sample and buffer plates.

FIG. 2 shows a right-front view of the instrument with one drawer pulledout for placement of a buffer plate and the top and side doorcompartments open.

FIG. 3 shows the x-z stage assembly.

FIG. 4 shows a drawer, stage assembly, tray holder, and sample plate.

FIG. 5 shows the bottom of a tray holder.

FIG. 6 shows a right-side view of the instrument without the cover.

FIG. 7 shows the left-side view of the instrument without the cover.

FIG. 8 shows a capillary array cartridge.

FIG. 9 shows the flowchart for the software control program for creatinga queue of jobs.

FIG. 10 shows a computer screen image of the computer software.

FIG. 11 shows the positioning of a sample plate under the array by thestage.

FIG. 12A shows a view of the capillary electrophoresis reservoir system.

FIG. 12B shows a view of the capillary electrophoresis reservoir system.

FIG. 13A shows a view of the x-z stage relative to the drawers.

FIG. 13B shows a view of the x-z stage with a sample tray lifted.

FIG. 14A shows a top view of a 384-well plate.

FIG. 14B shows the top view of a 96-well plate.

FIG. 15A shows a capillary array motion control system.

FIG. 15B shows the capillary array motion control system of FIG. 15Awithout the top sliding plate.

FIG. 15C shows the capillary array motion control system of FIG. 15Awith an array mounted.

FIG. 16A shows a view of a modified capillary array with the electrodesand capillaries bound together with heat shrink tubing.

FIG. 16B shows cross-sectional view of the capillary, electrode, andheat-shrink binding.

FIG. 17A shows a modified tray carrier with extensions that canautomatically push out or pull in a drawer.

FIG. 17B shows a modified tray carrier engaged with a drawer.

FIG. 18 shows the electrophoresis console, with drawers 4 and 5 replacedwith a plate.

DETAILED DESCRIPTION OF THE INVENTION

The invention is a multiplexed capillary electrophoresis system withenhanced workflow. The capillary electrophoresis system and apparatus ofthe present invention includes an absorbance or fluorescence-basedcapillary electrophoresis sub-system with a light source, a method forcarrying light from the light source to the sample windows of amultiplex capillary array containing at least 12 capillaries (preferably96 capillaries), and a method for detecting light emitted (fluorescence)or absorbed (absorbance) from the sample windows of a multiplex array.The sub-system also includes a method for pumping buffers and gelsthrough the capillaries, as well as a method for application of anelectric field for electrophoretic separation. The optics of thefluorescent-based sub system of the present invention are described byPang n United States Patent Applications 20070131870 and 20100140505,herein incorporated by reference in their entirety. The optics of anapplicable absorbance-based system, as well as the fluid handling,reservoir venting, application of electric field, and selection offluids via a syringe pump and a 6-way distribution valve are discussedby Kennedy et al. in U.S. Pat. Nos. 7,534,335 and 6,833,062, hereinincorporated by reference their entirety.

Referring to FIG. 1 the multiplex capillary system and/or console 16,with enhanced workflow has a door 10 for easy access to the loading ofgels, two drawers 11 for the easy loading of a buffer tray and a wastetray. Drawers 12 can be opened for easy loading of 96 or 384 well PCRplates, tube strips, vials, or other sample containers. A top door 13can be opened to access a replaceable capillary array, array window, andreservoir. An indicator light 14 is used to for notifying users of theactive application of a high-voltage for electrophoresis. A removableback-panel 15 allows access to electronics such as a high-voltage powersupply, electrical communication panels, a pump board, pressuretransducer board, and stage driver electronics. The back panel 15 alsoallows maintenance access to the x-z stage, which is used to move sampletrays from the drawers 11 and 12 to a capillary array.

FIG. 2 shows the multiplex capillary system used with the enhancedworkflow console 16 with the top and side doors open. A replaceablecapillary array 17 holds either 12 or 96 capillaries for multiplexcapillary electrophoresis. An LED light guide 67 guides light from a LEDengine located in the back compartment to the array window block 22which is inserted between the array window holder 19 and LED light guideand window holder 18. In this view, array window block 22 is attached tothe capillary array 17 for display. When the capillary array is removed,from the system, the array window block 22 can be attached to thecapillary array 17 (as shown). When the capillary array is fullyinstalled, the array window block 22 is not visible because it issandwiched between the array window holder 19 and LED light guide andwindow holder 18. A vent valve 21 is connected to the top of a capillaryreservoir 20. A syringe pump 23 coupled with a 6-way distribution valve29 delivers fluids and electrophoresis gels from fluid containers 24 and25 into the capillary reservoir 20, waste container 26, or capillariesin the capillary array 17. A fan 27 is used for forcing cool air fromthe back compartment through the capillary array 17, past the outside ofthe reservoir 20, down past the fluid containers 24, 25 and finally outthe bottom of the instrument. LED indicator lights 120 are used toindicate the presence or absence of trays in the drawers. A buffer tray28 is shown in a drawer (11, FIG. 1). The capillary array reservoir tip91 is shown inserted into the reservoir 20.

The concepts and practical implementation of motion control systems areknown. For example, Sabonovic and Ohnishi; “Motion Control” John Wileyand Sons, 2011, herein incorporated by reference in its entirety,discusses practical methods for the design and implementation of motioncontrol. It does not, however, show an enhanced CE workflow console 16as depicted here.

FIG. 3 shows the x-z stage assembly 48, which is used to transportsample trays (50, FIG. 4) and associated tray holders (51, FIG. 4) fromthe drawers (12 FIG. 1) to the injection capillaries (72, FIG. 8) andinjection electrodes (71, FIG. 8) of the capillary array (17, FIG. 8).The x-z stage assembly 48 is also used to position a buffer tray orwaste tray (28, FIG. 2) from the drawers (11, FIG. 1) to the injectioncapillaries and electrodes of the capillary array (72, FIG. 8). The x-zstage assembly has a tray carrier 31 with alignment pins 32, which alignwith holes (57, FIG. 5) on the bottom of the tray holder (51, FIG. 4) toprevent subsequent sliding or movement of the tray holders duringtransport. A protective cover 34, made of metal or plastic, is used toprevent gels or other liquids from spilling onto the x-direction guiderails 38 and x-direction drive belt 37 of the stage assembly. An x-drivestepper motor 35 is used as the electro-mechanical driver for motion inthe x-direction. A drive pulley 36 is attached to the stepper motor 35and x-direction drive belt 37 which drives the stage carrier 39 back-andforth along the guide-bars 38. A second drive pulley (not shown) is usedon belt 37 towards the back-end of the stage, which allows the belt tomake a full loop when affixed to stage carrier 39. Any motor-inducedmovement of the belt induces an x-direction movement of the stagecarrier 39 on the guide rails 38. A stepper-motor for the z-position islocated at 41, which is attached to a drive pulley/belt configurationsimilar to that shown in the x-direction. The x-direction drive belt isshown as 43. The z-position motor/pulley/belt is used to move the traycarrier 31 up and down the guide bars 40. Top plate 33 serves as astructural support for the guide bars 40. An electrical communicationstrip 44 is used to communicate between an electrical motor controlboard 46 and the stepper motors 41 and 35. An x-direction membranepotentiometer strip 49, along with appropriate control electronics, isused to determine and control the absolute position of the stage carrier39 in the x-direction. A z-direction membrane potentiometer strip 42,along with appropriate control electronics, is used to determine theabsolute position of the tray carrier 31 in the z-direction. Linearencoders or rotational encoders (on the stepper motor) are alternativeforms of positional measurement and control. Bearings 45 are located oneach guide bar 40 and guide rail 38 to enable friction-free movement ofboth the tray carrier 31 and the stage carrier 39. Note that there aretwo guide bars or guide rails per axis. Electrical cord guide straps 47are attached to a back support, which also holds the electrical controlboard 46 for the x-z stage assembly.

FIG. 4 shows a drawer 12, superimposed on an image of the stage assembly48, tray holder 51, and 96-well sample tray 50. The tray holder 51 ismolded to specifically hold a 96-well plate, shown here as 50.Alternative moldings of the tray holder allow for different sampleplates, including 384-well plates. Holes (57, FIG. 5) on the bottom ofthe tray holder 51 align with the alignment pins 32 of the tray carrier(31 FIG. 4). Notches 53 in the tray holder 51 align with alignment pins52 on the drawer 12 to enable the tray holder to fit in a tight,reproducible way within the sample drawer.

FIG. 6 Shows a right side view of the electrophoresis system, with achassis 66, pump motor and control system 61, pump control board 62, LEDlight engine 69, LED light line 67, high voltage power supply board 65,capable of applying 0.0 kV to 15 kV across the electrodes of the array,a CCD camera 64, capillary array cartridge 17, array window holder 19,reservoir 20, drawers 11, drawers 12, fluid lines 68, waste container26, gel containers 25 and syringe 23. A USB electronic distribution bardis shown as 63.

FIG. 7 shows a left side-view of the electrophoresis unit showing thex-z stage assembly 48, which moves tray holders 51 and sample trays 50from a drawer 12 or 11 to the bottom of array 17. The stage unit 48 canmove the sample tray holder 51 and sample tray 50 up in the z-directionto lift the tray holder/sample tray off of the drawer, move back in thex-direction away from the sample drawers, and then move the sample plateup in the z-direction to the bottom of the capillary array 17. Afterelectrokinetic or hydrodynamic injection, the stage unit 48 can move thesample tray holder/sample tray back down to the target drawer position(down in the z-direction), move forward in the x-direction just abovethe sample plate, and then drop down in the z-direction to set thesample tray holder/sample tray onto the drawer. When the sample trayholder 51 is resting in a drawer, the back edge of the sample trayholder 51 and sample tray 50 are aligned so that they do not liedirectly underneath the array 17. This allows the sample stage traycarrier (31, FIG. 3) to move up and down along the entire z-axis with atray holder/sample tray without colliding into other tray holders/sampletrays in the drawers. The alignment pins (70, FIG. 8) on the bottom ofarray 17 are used to align the tray holder with a tray so that thecapillary and electrode tips dip into each sample well of the sampleplate and do not collide with other areas of the sample plate. This isshown in more detail in FIG. 11, which shows a sample tray holder 51with a sample tray 50 aligned underneath a capillary array. Alignmentholes 56 on the tray holder 51 force the alignment of the tray holderwith the capillary array alignment pins 70.

FIG. 7 also shows high voltage power supply board 65 and high voltagepower supply cable (to the array) 75.

FIG. 8 shows an array cartridge 17, with rigid plastic support structure77, window storage and transport screw 80, capillary support cards 76,high voltage power supply cable 75, and insulating support structure 73onto which the electric circuit board 74 is placed. Electrodes, 71protrude through the electric circuit board 74, through the insulatingsupport structure 73, and protrude through the bottom of the array. Theelectrode material is stainless steel or tungsten. The electrodedimension, which is not a critical aspect of the invention, is 50 mmdiameter times 29 mm length. The protrusion from the bottom of thecartridge base is 20.0 mm. The electrodes are soldered onto the circuitboard 74. The high voltage power supply cable 75 is also soldered to thesame circuit of the electrical circuit board, which enables contact ofthe electrodes 71 with the high voltage power supply (65, FIG. 6).Capillary tips 72 are threaded through the electric circuit board 74 andinsulated support structure 73 and are aligned immediately adjacent andparallel to the electrode tips. The distance between the capillary tipsand electrodes are from 0.1 mm to 4 mm. The ends of the capillaries andthe ends of the electrode lie in a single plane (i.e. the capillary tipsand electrode tips are the substantially the same length, with lengthvariation of no more than about +/−1 mm. Preferably, the lengthvariation of capillary tips and electrode tips is less than 0.5 mm. Thecapillaries thread through the bottom of the capillary array, throughthe insulating support structure 73, through the electric circuit board74, through the capillary support cards 76 (which are supported by therigid plastic support structure 77) through the capillary window holder70 with capillary windows 79 centered in the opening of the windowholder, and then finally through the capillary reservoir tip 91, inwhich all capillaries (in this case 12) are threaded through a singlehole. For 96 capillary arrays, capillaries are threaded in groups of 12,or preferably groups of 4 in the capillary reservoir tip 79. Thecapillaries are held in place in the reservoir tip 91 with an adhesive,such as a thermally or uv-curable epoxy.

FIG. 12A shows the reservoir, with reservoir body 20, capillaryreservoir tip 91, slider bar 130 (for locking capillary reservoir tipinto the reservoir, through alignment of a notch on the capillaryreservoir tip 91 and the slider bar 130), vent block valve 21, wastetube out 138, waste block valve 132, and pressure transducer cavity 133.

FIG. 12B shows an alternate cut-out view of the reservoir, withreservoir body 20, capillary reservoir tip 91, slider bar 130, ventblock valve 21, waste tube out 138, waste block valve 132, electrode forattachment to ground 135, pressure transducer cavity 133, pressuretransducer 136, pressure transducer cable for attachment toanalog/digital board 137, and fluid tube input 134 (from syringe pump 23FIG. 2).

The reservoir body can be made of any solid material such as acrylic,Teflon, PETE, aluminum, polyethylene, ABS, or other common metals orplastics. The key criterion is that the material is durable andchemically resistant to the materials used. A preferred material isacrylic or Teflon.

FIG. 13A shows the x-z stage unit 48 in relation to the drawers 11 and12. The x-z stage is located directly behind the drawers, and can movethe stage carrier (39, FIG. 13B) back-and forth in the x-direction usingthe stepper-motor for the z-position 41. A sample tray is removed from adrawer by first moving the stage forward, towards the drawers, in thex-direction. The tray carrier (31, FIG. 3) lifts a tray holder up andoff a drawer in the z-direction using the z-direction stepper motor (41,FIG. 3). The stage carrier is then moved back in the x-direction, awayfrom the drawers, as shown in FIG. 13B. The stage carrier 39 is thenmoved up in the z-direction to move the tray holder 51 and sample tray50 to the injection position of the capillary array (FIG. 11).

For the following discussion, the term “forward” means a forward motionof the x-z stage towards the drawers. The term “aft” means a backwardmotion, towards the back of the instrument (away from the drawers). Twosideways motions “right” and left” are perpendicular to the forward andaft motions and are achieved with an array stage. Combined, the x-zstage with the forward and aft motion, and the array stage, with thesideways motions “right” and “left” enable a sampling of a 384 wellplate with a 96-capillary array.

Also, for the following discussion, a 96-capillary array has a pluralityof capillaries and electrodes that exactly match the center of each wellin a 96-well plate, which is shown in FIG. 14B, (i.e. there are 96capillaries, with 96 corresponding electrodes, with the specialdimension of a 96-well plate as shown in FIG. 8 (12 capillaries onlyshown). Sampling a 384 well plate is performed using a 96-capillaryarray, with four individual 96-well injections per 384 well plate. Toperform this operation, the system must move the plate either forward,aft, or sideways (left or right) so that the capillaries and electrodesin the 96-capillary array can access all 384 wells of the plate. FIG.14A shows a top view of a 384 well plate. The center of the holesmeasure 4.5 mm from each other (i.e. the center of the first well of rowdefined by 142 is 4.5 mm from the center of well 143). There are 24columns and 16 rows for a total of 384 well positions. The first row is“A”, the second row is “B” (FIG. 14A 141), the 23^(rd) row is “0” (FIG.14A 142) and the 16^(th) row is “P (FIG. 14A 143). For sampling the 384well plate, a standard 96-capillary array has capillaries lined up infour possible positions:

Position 1: Wells A1, A3, . . . A23 to O1, O3, . . . O23.

Position 2: Wells A2, A4, . . . A24 to O2, O4, . . . O24.

Position 3: Wells B1, B3, . . . B23 to P1, P3, . . . P23.

Position 4: Wells B2, B4 . . . B24 to P2, P4, . . . P24.

For the capillary electrophoresis system of the present invention tosample a 384 well plate with a 96-capillary array there are severalpossible scenarios. Two of these scenarios are outlined below.

Scenario 1: In the sample plate holder (51, FIG. 4) Well A1 of a 96-wellplate (145, FIG. 14B) lines up exactly with well A1 of a 384 well plate(FIG. 14A). To move from Position 1 to Position 3 of the 384 well platerequires the system to move the tray forward by 4.6 mm (or theappropriate spacing between rows of a 384 well plate). This is performedwith the x-z stage 48 (FIG. 3). To move from position 3 to position 4requires the system to move the array left by 4.5 mm. This is performedby moving the array sideways, rather than the plate, using an arraymechanical stage 150, which is described below, and in FIGS. 15A, 15B,and 15C. Different 384 well plates may have different hole spacing, andthus require different forward and sideways distances, but the conceptis the same: Forward and aft motion is achieved by the mechanical stage48, and sideways (left and right) motion of the array is achieved by thearray stage 150. Access to all 384 wells of a 384 well plate with a 96capillary array requires two degrees of freedom. One degree of freedomis provided by moving the stage forward and aft, and the other degree offreedom is provided by moving the stage sideways left and right.

Scenario 2: In a sample plate holder (51, FIG. 4) well A1 of a 96 wellplate (145, FIG. 14B) lines up exactly in the center of Well A1, A2, B1and B2 (FIG. 14A, 144) of a 384 well plate.

In this scenario for sampling a 384 well plate with a 96-capillaryarray, the default position of the 96-capillary is such that CapillaryA1 lines up exactly with a 96-well plate well A1 (FIG. 14B 145), whichalso corresponds to the center point 144 between wells A1, A2 B1 and B2of the 384 well plate. To sample Position 1 of the 384 well platerequires the x-z stage 48 to move the tray forward by 2.25 mm, and tomove the array to the left by 2.25 mm using array stage 150. To samplePosition 2 of the 384 well plate (from the default starting position)requires the x-z stage 48 to move the stage forward by 2.25 mm and thearray to the right 2.25 mm using stage 150. To sample Position 3 of the384 well plate (from the default starting position) requires the x-zstage 48 to move the tray aft by 2.25 mm and the array to the left 2.25mm using stage 150 (below). To sample Position 4 of the 384 well plate(from the default starting position) requires the x-z stage 48 to movethe stage aft by 2.25 mm and the array to the right 2.25 mm using stage150 (below). FIG. 15 shows a view of a capillary array mechanical stage150, which, when coupled with the x-z mechanical stage 48 enables accessto all 384 wells of a 384 well plate using a 96-capillary array. Plate151 is mounted and permanently fixed on the capillary electrophoresissystem, and allows for connection of the capillary array. Sliding plate152, which is smaller than Plate 151, rests on top (and within) plate151 and is allowed to move back and forth by sliding, leaving gap 153when moved to one side of the plate 151. A stepper motor, coupled withthe appropriate software control, 154 moves or slides plate 152, viaconnection-bridge 155. A linear membrane potentiometer 156, coupled withbridge pressure connector 157 monitors the position of sliding plate 152resting within plate 151, and allows for precise location control ofplate 152. Pressure contact between the linear membrane potentiometer156 and plate 152 is achieved through a bridge pressure connector 157.Plate 151 contains bearings 158, on which plate 152 rests upon, andwhich allow for low-friction movement when plate 152 moves fromside-to-side. To assist in positioning the 96-capillary array on the 384well plate, contained in plate holder 53, alignment holes 159 aremodified to allow for four individual positions of the 96-capillaryarray on the 384 well plate.

FIG. 15C shows the same array mechanical stage 150 shown in FIG. 14,with an array 17 mounted in the slider plate 152.

FIG. 15B shows plate 151, with the exposed bearings 158 on which plate152 sits upon. These bearings allow for back-and-forth sliding movementof plate 152 on top of plate 151 with reduced friction,

In order to reliably insert a 96-well capillary array into the wells ofa 384 well plate, it is necessary to bind the electrodes and capillariestogether, so that either the capillaries or electrodes do not collidewith the sides of the wells of the 384 well plates. FIG. 16A Shows anexpanded portion of a modified 96-capillary array, with capillaries 72,bound to electrodes 71 by heat-shrink tubing 160. FIG. 16B shows across-section of the bound capillary-electrode, showing capillary 72,electrode, 71 and heat-shrink tubing 160. The length or placement of theheat shrink tubing is such that it does not overlap the ends of thecapillaries or electrodes. Alternate methods for binding the electrodesto the capillaries are also acceptable, including the use of adhesivesor epoxies.

Although the intent is to eliminate the need for external robots, thegeometry and configuration of the electrophoresis console of the presentinvention is ideally suited for interfacing to an external robotic arm.

The tray carrier 31 of the x-z-stage shown in FIG. 3 is modified toengage the drawers, so that the stage can push out or pull in drawers.The drawers may contain a sample plate, so that a robotic arm may removeor exchange a sample plate from the system once the plate is pushed outby the x-z stage. Alternately, the x-z stage may push out an empty trayso that a robotic arm may put a new tray into the system. The x-z stagecan pull the drawers back into the system, disengage the drawer, andthen transport trays to the arrays, as described above.

FIG. 17A shows a segment of x-z stage with a tray carrier 31 that ismodified with two extensions 170 that fit into slots 171 within thedrawer. FIG. 17B shows the same tray carrier 31 that is fully engagedwith the drawer, allowing the x-z stage to push the drawer out or pullthe drawer in.

The stage carrier extensions 170 engage the drawer by moving directlyover and then down into the slots 171 in the drawer. The stage carriercan move the drawer forward and aft without disengagement from thedrawer. To disengage from the drawer, the tray carrier 31 is moved up toslide the extensions out of the slot. The tray carrier is then free totransport trays to the array for electrophoresis or storage.

FIG. 18 shows the electrophoresis console of the present invention,where the drawers 4 and 5 have been removed and replaced with a flatplate 180. This flat plate allows more room for robotic arms, ifnecessary.

A typical strategy for pumping fluids for capillary electrophoresis isas follows. Consider the following 6 positions of the six-waydistribution valve (29, FIG. 2) on the syringe. Position 1 is connectedto the bottom of the reservoir (134, FIG. 12B); position 2 is connectedthrough a tube to a bottle of conditioning fluid (a fluid forconditioning the walls of the capillaries); position 3 is connected to a“Gel 1” which is used for the analysis of genomic DNA, position 4 isconnected to a “Gel 2” which is used for the analysis of fragmented DNA,position 5 is unused, or optionally used to clean the vent valve via thepumping of air through the vent valve to the waste bottle and position 6is connected to the waste bottle.

Step A: The reservoir is first emptied by opening position 1(reservoir), filling the syringe with fluid that is in the reservoir,closing position 1, opening position 6, and emptying fluid to the waste.This is repeated until the reservoir is empty. Block valves 21 and 132are kept open during this process to enable efficient draining of thereservoir.

Step B: The reservoir is then filled with conditioning solution byopening position 2, filling the syringe with conditioning solution,closing position 2, opening position 1, and filling the reservoir withconditioning solution. Block valve 21 is closed, but block valve 132 towaste is open, enabling the over-filling of the reservoir withconditioning solution.

Step C: The capillaries are filled by closing both vent block valve 21and waste vent valve 132. The syringe is filled with capillaryconditioning solution. Position 1 is opened, and fluid is pressurefilled through the capillaries at a minimum of 100 psi for apre-determined time, which may range from 1 minute to 20 minutes.

Step D: The reservoir is emptied by step A, and then re-filled with gelusing the same process as in Step B, except that position 3 for the gelis used on the 6-way distribution valve.

Step E: The capillaries are filled with gel using a process analogous toStep C.

After steps A-E, the capillaries are ready for electrophoresis.

A general strategy and process for analyzing samples usingelectrophoresis is as follows.

Samples are placed into a 96-well plate for analysis. The user placesthe sample plate into a sample drawer (12, FIG. 1), and then adds jobsto a computer-based queue, corresponding to the analysis of a specificrow or the entire sample plate in the drawer. The computer, which is thecontrol system of the instrument, executes the analysis of the row orentire tray of interest.

A key embodiment of the invention is the workflow of the capillaryelectrophoresis system. Drawers (11, FIG. 1) allow easy placement ofbuffer and waste trays into the system. Drawers (12, FIG. 1) allow easyplacement of sample trays into the system. Of particular importance isthe ability to place or remove sample trays from drawers (12, FIG. 1)while the system is performing capillary electrophoresis. Indicatorlights (120, FIG. 1) show if a tray is present or absent in a drawer,which let users know if a drawer is in place. A typical workflow for a12-capillary multiplex system is as follows: User A walks up to themachine with sample tray 1, and places it into the third drawer from thetop (one of drawers 11, FIG. 1). User “A” then fills a queue with threejobs, which correspond to performing capillary electrophoresis on thethree rows of samples: sample tray 1 row A, sample tray 1 row B, andsample tray 1 row C. User “A” then instructs the computer to execute thequeue, and as a result, the system begins capillary electrophoresis ofsample tray 1, row A, and will continue executing jobs in the queueuntil there are no more jobs. User “B” then comes up and places sampletray 2 into the fourth drawer from the top (one of drawers 11, FIG. 1).User “B” then adds 8 jobs to the queue corresponding the performing ofcapillary electrophoresis on 8 rows of samples: sample tray 2, rows A-H.The computer will continue analyzing user “A” samples until they arefinished, and then continue on with the analysis of user “B” samples. Inthe meantime, user “C” walks up and loads sample tray 3 into the fifthdrawer from the top (one of drawers 11, FIG. 1). User “C” then adds 1job to the queue corresponding to the analysis of 1 row of samples:sample tray 3, row A. This process can continue indefinitely, as long asthere is sufficient gel in gel containers (25 in FIG. 2), or if there issufficient run buffer in the buffer tray (28, FIG. 2) located in topdrawer 11, FIG. 1. It is, among other things, the enabling of thisworkflow, via the drawers sample stage, and computer program with aqueue for loading jobs that differentiates the present invention fromthe prior art systems for CE workflow.

An important embodiment of the present invention is a computer programthat enables users to load a sample plate into the desired verticaldrawer (12, FIG. 1), and instruct the system to run the desired rows orentire sample plate, while the system is running other samples. Thisallows multiple users to load samples and/or sample plates, or a singleuser to load multiple samples and/or sample plates without first havingto wait for the electrophoresis of other samples to be complete.

FIG. 9 shows the general flow diagram of the work process and computerprogram. A user loads a sample tray into a drawer (12, FIG. 1) of thesystem. On the computer, user then selects the tray, edits sample namesand/or tray name. User further selects or defines a method (time ofseparation, electric field used for separation, gel selection, etc.).This selected tray, along with an associated method is defined as a“job”, which is then placed into a queue. The computer as an instrumentcontrol device, fetches jobs from the queue, and controls the instrumentfor every task, including operation of the syringe pump, operation ofthe high voltage power supply, and the motion control stage (48, FIG.3). For each run (or job), there may be a variety of tasks, with eachtask requiring direct command and control of subunits of the system.Tasks associated with control of the syringe pump includeemptying/filling the reservoir with conditioning fluid, forcingconditioning fluid through the capillaries, emptying/filling thereservoir with gel, forcing gel through the capillaries. Tasksassociated with control of the x-z stage may include moving or removinga waste tray to/from the inlet capillaries and electrodes of thecapillary array, moving or removing a buffer tray to/from the inletcapillaries and electrodes of the capillary array, or moving/removing asample tray to/from the inlet capillaries and electrodes of thecapillary array. Tasks associated with control of the high voltage powersupply include turning off/on a high voltage for capillaryelectrophoresis separation. Other tasks are associated with the camera(acquisition of data), and block valves. For each set of samples, theprogram will complete all tasks required to obtain a set ofelectropherograms. Once these tasks are complete, the program fetchesanother job from the queue. If the queue is empty, all sample runs arecomplete (until the user initiates another queue).

The graphical result of this computer program is shown in FIG. 10, whichshows a list of samples to be analyzed in queue 101, an option to addrows or trays to the queue 102, and an option to select the tray numberfor analysis 103. It is these three aspects that are critical tosoftware portion of the invention: a) Selection of tray 103(corresponding to a drawer 11 FIG. 1) b) Adding the sample set to aqueue (102, FIG. 10) and c) A queue of active samples for analysis (101,FIG. 10), which are executed in sequence until all jobs are complete.Another critical aspect is the ability to add samples to instrumentdrawers (11, FIG. 1) and queue (101, FIG. 10) while the instrument isrunning other samples.

As can be seen from the above description, the system eliminates theneed for expensive robots, enables the user to run many samples per day,allows loading of new samples while running others, and yet has a smallsize footprint.

What is claimed is:
 1. A multiplex capillary electrophoresis systemcapable of interfacing with an external robotic system, the multiplexcapillary electrophoresis system comprising: a console comprising aninjection position; a replaceable multiplex capillary array disposed inthe console, and comprising a plurality of capillaries comprisingrespective capillary tips disposed at the injection position; a powersupply disposed in the console and configured to apply a voltage acrosseach of the capillaries effective for performing capillaryelectrophoresis on a sample in one or more of the capillaries; aplurality of drawers disposed in the console and configured to hold aplurality of multi-well plates for containing the sample or buffer, eachdrawer movable between a closed position inside the console and an openposition outside the console at which the drawer is externallyaccessible by the robotic system; and a motion control system disposedin the console and comprising a movable stage assembly, wherein: themovable stage assembly is configured to move at least one of themulti-well plates from at least one of the drawers to the injectionposition; and the movable stage assembly is configured to releasablyengage the at least one drawer and push the at least one drawer from theclosed position to the open position or pull the at least one drawerfrom the open position to the closed position, and thereby allow theexternal robotic system to place one or more multi-well plates onto theat least one drawer or remove the one or more multi-well plates from theat least one drawer.
 2. The multiplex capillary electrophoresis systemof claim 1, wherein the plurality of drawers comprises at least fourvertically stacked drawers.
 3. The multiplex capillary electrophoresissystem of claim 1, wherein the plurality of drawers comprises at leastsix vertically stacked drawers.
 4. The multiplex capillaryelectrophoresis system of claim 1, wherein the movable stage assemblycomprises an extension configured to engage with and disengage from theat least one drawer to push the at least one drawer from the closedposition to the open position or pull the at least one drawer from theopen position to the closed position.
 5. The multiplex capillaryelectrophoresis system of claim 4, wherein the at least one drawercomprises a slot and the extension is configured to releasably fit intothe slot.
 6. The multiplex capillary electrophoresis system of claim 4,wherein the movable stage assembly comprises a tray carrier configuredto support a selected multi-well plate of the plurality of multi-wellplates, and the tray carrier comprises the extension.
 7. The multiplexcapillary electrophoresis system of claim 1, wherein the movable stageassembly comprises a tray carrier configured to support a selectedmulti-well plate of the plurality of multi-well plates.
 8. The multiplexcapillary electrophoresis system of claim 7, wherein the movable stageassembly comprises an x-drive motor configured to drive motion of thetray carrier horizontally back and forth relative to the drawers, and az-drive motor configured to drive motion of the tray carrier verticallyup and down relative to the drawers.
 9. The multiplex capillaryelectrophoresis system of claim 7, wherein the tray carrier comprisesone or more alignment pins configured to engage a tray holder of theselected multi-well plate.
 10. The multiplex capillary electrophoresissystem of claim 1, wherein each drawer comprises one or more alignmentpins configured to engage a tray holder of the selected multi-wellplate.
 11. The multiplex capillary electrophoresis system of claim 1,comprising an array stage on which the multiplex capillary array isdisposed and configured to move the multiplex capillary array in ahorizontal left and right direction.
 12. The multiplex capillaryelectrophoresis system of claim 11, wherein the movable stage assemblyis configured to move the at least one multi-well plate in a horizontalforward and aft direction orthogonal to the left and right direction.13. The multiplex capillary electrophoresis system of claim 11, whereinthe array stage comprises a sliding plate on which the multiplexcapillary array is disposed, and an array stage motor configured todrive motion of the sliding plate in the left and right direction. 14.The multiplex capillary electrophoresis system of claim 1, comprising aplurality of injection electrodes communicating with the power supplyand disposed adjacent and parallel to the capillary tips.
 15. Themultiplex capillary electrophoresis system of claim 14, wherein eachinjection electrode is bound together with a corresponding one of thecapillaries.
 16. The multiplex capillary electrophoresis system of claim14, comprising a plurality of tubes, each tube binding together acorresponding one of the injection electrodes and the capillaries.